The present invention relates to the field of mass spectrometry and in particular to the detection and identification of post translationally modified peptides using a mass spectrometer.
Peptides consist of 20 commonly occurring amino acids that are linked together via amide bonds during the process of translating the mRNA message into protein sequence. The post translational modification of these polypeptides is ubiquitous and it is now widely understood and accepted that these modifications often infer biological function. There are a considerable number of modifications that occur, with common modifications including phosphorylation, glycosylation, myristylation, acetylation, methylation and ubiquinylation.
Tandem quadrupole mass spectrometers are widely used in a variety of industries. A known tandem quadrupole mass spectrometer comprises a first resolving quadrupole mass filter (MS1) followed by a gas filled collision cell arranged downstream of the first quadrupole mass filter. A second resolving quadrupole (MS2) is arranged downstream of the collision cell. Historically, the collision cell has often comprised a non-resolving quadrupole rod set leading to these instruments being known as “triple quadrupoles”.
A common mode of operation of a tandem quadrupole mass spectrometer is known as Multiple Reaction Monitoring (“MRM”), wherein the first quadrupole mass filter MS1 is set to transmit only a pre-determined precursor or parent ion which is then fragmented in the collision cell. The resultant fragment ions are then transmitted to the second quadrupole mass analyser MS2 which is operated as a mass filter and is set so that only a single predetermined fragment ion is transmitted onwards to the ion detector. The resultant signal that is detected is therefore highly specific and highly sensitive.
Another common mode of operation of the known tandem quadrupole instrument is known as “precursor or parent ion scanning” wherein the first quadrupole mass filter MS1 is scanned across a chosen mass range with the transmitted ions being fragmented in the collision cell. The second quadrupole mass filter MS2 is set to transmit a fixed fragment mass. The resultant mass spectrum contains only those precursor or parent ions that fragmented to give the chosen fragment ion. Again, this is a highly specific and sensitive mode of operation.
A further mode of operation is known as “daughter or product ion scanning” or MS/MS wherein the first quadrupole MS1 is set to transmit a chosen precursor or parent ion which is subsequently fragmented in the collision cell. The second quadrupole mass filter MS2 is then scanned across a chosen mass range to allow a mass spectrum of the daughter or product ions to be acquired.
A MS scan is where either MS1 is set to resolve and is scanned with MS2 not resolving or vice versa. A MS scan generates a spectrum of all of the parent or precursor ions.
Several MS based approaches to the detection and sequencing of PTM peptides are known. These incorporate both infusion based and liquid chromatography based separation strategies, in combination with a variety of MS instrument geometries, such a tandem quadrupole systems and hybrid quadrupole-Time of Flight mass analyser systems. It is known, for example, to use precursor ion scanning looking for a common structural motif on a tandem quadrupole based system. However, there are several problems with the known approaches. Increasingly, the approaches have to be compatible with nanoscale liquid chromatography separations having narrow peak widths (of between 4-10 seconds). This demands that a complete analytical cycle of the experiment take no longer than one second to ensure adequate points across the chromatographic peak. This is not true of most known approaches. Secondly, brute force approaches have been used to try and sequence all peptides and sort the modified peptides from the non-modified peptides. This is highly time consuming and involves acquiring a considerable amount of redundant MS/MS information.
A specific, rapid technique with high sensitivity is desirable to detect and characterise post translationally modified peptides.
It is therefore desired to provide an improved mass spectrometer and method of mass spectrometry.